forked from D-Net/dnet-hadoop
37 lines
588 KiB
HTML
37 lines
588 KiB
HTML
|
<html lang="en"><head>
|
||
|
|
<meta charset="utf-8">
|
||
|
|
<title>PED</title>
|
||
|
|
<base href="/">
|
||
|
|
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||
|
|
<link rel="apple-touch-icon" sizes="180x180" href="/assets/favicon/apple-touch-icon.png?v=zX7QdpMe85">
|
||
|
|
<link rel="icon" type="image/png" sizes="32x32" href="/assets/favicon/favicon-32x32.png?v=zX7QdpMe85">
|
||
|
|
<link rel="icon" type="image/png" sizes="16x16" href="/assets/favicon/favicon-16x16.png?v=zX7QdpMe85">
|
||
|
|
<link rel="manifest" href="/assets/favicon/site.webmanifest?v=zX7QdpMe85">
|
||
|
|
<link rel="mask-icon" href="/assets/favicon/safari-pinned-tab.svg?v=zX7QdpMe85" color="#1e74a5">
|
||
|
|
<link rel="shortcut icon" href="/assets/favicon/favicon.ico?v=zX7QdpMe85">
|
||
|
|
<meta name="msapplication-TileColor" content="#2b5797">
|
||
|
|
<meta name="msapplication-config" content="/assets/favicon/browserconfig.xml?v=zX7QdpMe85">
|
||
|
|
<meta name="theme-color" content="#ffffff">
|
||
|
|
<!-- Google Analytics -->
|
||
|
|
<script async="" src="https://www.google-analytics.com/analytics.js"></script><script>
|
||
|
|
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
|
||
|
|
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
|
||
|
|
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
|
||
|
|
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
|
||
|
|
ga('create', 'UA-178440005-1', 'auto');
|
||
|
|
ga('send', 'pageview');
|
||
|
|
</script>
|
||
|
|
|
||
|
|
<script type="text/javascript" src="https://apicuron.org/assets/apicuron-widget.js"></script>
|
||
|
|
|
||
|
|
<!--Twitter widget-->
|
||
|
|
<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
|
||
|
|
<link rel="stylesheet" href="styles.90962b8b9cc0103bb484.css"><style>.nav-bar[_ngcontent-eul-c97]{position:fixed;z-index:99;top:0;padding:0}.container[_ngcontent-eul-c97]{min-height:70vh}</style><style>@charset "UTF-8";
|
||
|
|
[_ngcontent-eul-c95]:root{--blue:#007bff;--indigo:#6610f2;--purple:#6f42c1;--pink:#e83e8c;--red:#dc3545;--orange:#fd7e14;--yellow:#ffc107;--green:#28a745;--teal:#20c997;--cyan:#17a2b8;--white:#fff;--gray:#6c757d;--gray-dark:#343a40;--primary:#007bff;--secondary:#6c757d;--success:#28a745;--info:#17a2b8;--warning:#ffc107;--danger:#dc3545;--light:#f8f9fa;--dark:#343a40;--breakpoint-xs:0;--breakpoint-sm:576px;--breakpoint-md:768px;--breakpoint-lg:992px;--breakpoint-xl:1200px;--font-family-sans-serif:-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";--font-family-monospace:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace}*[_ngcontent-eul-c95], [_ngcontent-eul-c95]:after, [_ngcontent-eul-c95]:before{box-sizing:border-box}html[_ngcontent-eul-c95]{font-family:sans-serif;line-height:1.15;-webkit-text-size-adjust:100%;-webkit-tap-highlight-color:rgba(0,0,0,0)}article[_ngcontent-eul-c95], aside[_ngcontent-eul-c95], figcaption[_ngcontent-eul-c95], figure[_ngcontent-eul-c95], footer[_ngcontent-eul-c95], header[_ngcontent-eul-c95], hgroup[_ngcontent-eul-c95], main[_ngcontent-eul-c95], nav[_ngcontent-eul-c95], section[_ngcontent-eul-c95]{display:block}body[_ngcontent-eul-c95]{margin:0;font-family:-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Helvetica Neue,Arial,Noto Sans,sans-serif,Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol,Noto Color Emoji;font-size:1rem;font-weight:400;line-height:1.5;color:#212529;text-align:left;background-color:#fff}[tabindex="-1"][_ngcontent-eul-c95]:focus:not(:focus-visible){outline:0!important}hr[_ngcontent-eul-c95]{box-sizing:content-box;height:0;overflow:visible}h1[_ngcontent-eul-c95], h2[_ngcontent-eul-c95], h3[_ngcontent-eul-c95], h4[_ngcontent-eul-c95], h5[_ngcontent-eul-c95], h6[_ngcontent-eul-c95]{margin-top:0;margin-bottom:.5rem}p[_ngcontent-eul-c95]{margin-top:0;margin-bottom:1rem}abbr[data-original-title][_ngcontent-eul-c95], abbr[title][_ngcontent-eul-c95]{text-decoration:underline;-webkit-text-decoration:underline dotted;text-decoration:underline dotted;cursor:help;border-bottom:0;-webkit-text-decoration-skip-ink:none;text-decoration-skip-ink:none}address[_ngcontent-eul-c95]{font-style:normal;line-height:inherit}address[_ngcontent-eul-c95], dl[_ngcontent-eul-c95], ol[_ngcontent-eul-c95], ul[_ngcontent-eul-c95]{margin-bottom:1rem}dl[_ngcontent-eul-c95], ol[_ngcontent-eul-c95], ul[_ngcontent-eul-c95]{margin-top:0}ol[_ngcontent-eul-c95] ol[_ngcontent-eul-c95], ol[_ngcontent-eul-c95] ul[_ngcontent-eul-c95], ul[_ngcontent-eul-c95] ol[_ngcontent-eul-c95], ul[_ngcontent-eul-c95] ul[_ngcontent-eul-c95]{margin-bottom:0}dt[_ngcontent-eul-c95]{font-weight:700}dd[_ngcontent-eul-c95]{margin-bottom:.5rem;margin-left:0}blockquote[_ngcontent-eul-c95]{margin:0 0 1rem}b[_ngcontent-eul-c95], strong[_ngcontent-eul-c95]{font-weight:bolder}small[_ngcontent-eul-c95]{font-size:80%}sub[_ngcontent-eul-c95], sup[_ngcontent-eul-c95]{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sub[_ngcontent-eul-c95]{bottom:-.25em}sup[_ngcontent-eul-c95]{top:-.5em}a[_ngcontent-eul-c95]{color:#007bff;text-decoration:none;background-color:transparent}a[_ngcontent-eul-c95]:hover{color:#0056b3;text-decoration:underline}a[_ngcontent-eul-c95]:not([href]), a[_ngcontent-eul-c95]:not([href]):hover{color:inherit;text-decoration:none}code[_ngcontent-eul-c95], kbd[_ngcontent-eul-c95], pre[_ngcontent-eul-c95], samp[_ngcontent-eul-c95]{font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-size:1em}pre[_ngcontent-eul-c95]{margin-top:0;margin-bottom:1rem;overflow:auto;-ms-overflow-style:scrollbar}figure[_ngcontent-eul-c95]{margin:0 0 1rem}img[_ngcontent-eul-c95]{border-style:none}img[_ngcontent-eul-c95], svg[_ngcontent-eul-c95]{vertical-align:middle}svg[_ngcontent-eul-c95]{overflow:hidden}table[_ngcontent-eul-c95]{border-collapse:collapse}caption[_ngcontent-eul-c95]{padding-top:.75rem;padding-bottom:.75rem;color:#6c757d;text-align
|
||
|
|
[_ngcontent-eul-c96]:root{--blue:#007bff;--indigo:#6610f2;--purple:#6f42c1;--pink:#e83e8c;--red:#dc3545;--orange:#fd7e14;--yellow:#ffc107;--green:#28a745;--teal:#20c997;--cyan:#17a2b8;--white:#fff;--gray:#6c757d;--gray-dark:#343a40;--primary:#007bff;--secondary:#6c757d;--success:#28a745;--info:#17a2b8;--warning:#ffc107;--danger:#dc3545;--light:#f8f9fa;--dark:#343a40;--breakpoint-xs:0;--breakpoint-sm:576px;--breakpoint-md:768px;--breakpoint-lg:992px;--breakpoint-xl:1200px;--font-family-sans-serif:-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";--font-family-monospace:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace}*[_ngcontent-eul-c96], [_ngcontent-eul-c96]:after, [_ngcontent-eul-c96]:before{box-sizing:border-box}html[_ngcontent-eul-c96]{font-family:sans-serif;line-height:1.15;-webkit-text-size-adjust:100%;-webkit-tap-highlight-color:rgba(0,0,0,0)}article[_ngcontent-eul-c96], aside[_ngcontent-eul-c96], figcaption[_ngcontent-eul-c96], figure[_ngcontent-eul-c96], footer[_ngcontent-eul-c96], header[_ngcontent-eul-c96], hgroup[_ngcontent-eul-c96], main[_ngcontent-eul-c96], nav[_ngcontent-eul-c96], section[_ngcontent-eul-c96]{display:block}body[_ngcontent-eul-c96]{margin:0;font-family:-apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Helvetica Neue,Arial,Noto Sans,sans-serif,Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol,Noto Color Emoji;font-size:1rem;font-weight:400;line-height:1.5;color:#212529;text-align:left;background-color:#fff}[tabindex="-1"][_ngcontent-eul-c96]:focus:not(:focus-visible){outline:0!important}hr[_ngcontent-eul-c96]{box-sizing:content-box;height:0;overflow:visible}h1[_ngcontent-eul-c96], h2[_ngcontent-eul-c96], h3[_ngcontent-eul-c96], h4[_ngcontent-eul-c96], h5[_ngcontent-eul-c96], h6[_ngcontent-eul-c96]{margin-top:0;margin-bottom:.5rem}p[_ngcontent-eul-c96]{margin-top:0;margin-bottom:1rem}abbr[data-original-title][_ngcontent-eul-c96], abbr[title][_ngcontent-eul-c96]{text-decoration:underline;-webkit-text-decoration:underline dotted;text-decoration:underline dotted;cursor:help;border-bottom:0;-webkit-text-decoration-skip-ink:none;text-decoration-skip-ink:none}address[_ngcontent-eul-c96]{font-style:normal;line-height:inherit}address[_ngcontent-eul-c96], dl[_ngcontent-eul-c96], ol[_ngcontent-eul-c96], ul[_ngcontent-eul-c96]{margin-bottom:1rem}dl[_ngcontent-eul-c96], ol[_ngcontent-eul-c96], ul[_ngcontent-eul-c96]{margin-top:0}ol[_ngcontent-eul-c96] ol[_ngcontent-eul-c96], ol[_ngcontent-eul-c96] ul[_ngcontent-eul-c96], ul[_ngcontent-eul-c96] ol[_ngcontent-eul-c96], ul[_ngcontent-eul-c96] ul[_ngcontent-eul-c96]{margin-bottom:0}dt[_ngcontent-eul-c96]{font-weight:700}dd[_ngcontent-eul-c96]{margin-bottom:.5rem;margin-left:0}blockquote[_ngcontent-eul-c96]{margin:0 0 1rem}b[_ngcontent-eul-c96], strong[_ngcontent-eul-c96]{font-weight:bolder}small[_ngcontent-eul-c96]{font-size:80%}sub[_ngcontent-eul-c96], sup[_ngcontent-eul-c96]{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sub[_ngcontent-eul-c96]{bottom:-.25em}sup[_ngcontent-eul-c96]{top:-.5em}a[_ngcontent-eul-c96]{color:#007bff;text-decoration:none;background-color:transparent}a[_ngcontent-eul-c96]:hover{color:#0056b3;text-decoration:underline}a[_ngcontent-eul-c96]:not([href]), a[_ngcontent-eul-c96]:not([href]):hover{color:inherit;text-decoration:none}code[_ngcontent-eul-c96], kbd[_ngcontent-eul-c96], pre[_ngcontent-eul-c96], samp[_ngcontent-eul-c96]{font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-size:1em}pre[_ngcontent-eul-c96]{margin-top:0;margin-bottom:1rem;overflow:auto;-ms-overflow-style:scrollbar}figure[_ngcontent-eul-c96]{margin:0 0 1rem}img[_ngcontent-eul-c96]{border-style:none}img[_ngcontent-eul-c96], svg[_ngcontent-eul-c96]{vertical-align:middle}svg[_ngcontent-eul-c96]{overflow:hidden}table[_ngcontent-eul-c96]{border-collapse:collapse}caption[_ngcontent-eul-c96]{padding-top:.75rem;padding-bottom:.75rem;color:#6c757d;text-align
|
||
|
|
<body class="ng-tns-0-0">
|
||
|
|
<app-root _nghost-eul-c97="" ng-version="10.2.4"><div _ngcontent-eul-c97="" class="d-flex flex-column h-100"><div _ngcontent-eul-c97="" class="container-fluid" style="position: fixed; top: 0; z-index: 10;"><app-navbar _ngcontent-eul-c97="" _nghost-eul-c95=""><div _ngcontent-eul-c95="" class="row bg-dark page-header"><div _ngcontent-eul-c95="" class="container-fluid container-wide"><nav _ngcontent-eul-c95="" class="navbar navbar-expand-sm navbar-dark navbar-fixed-top"><a _ngcontent-eul-c95="" routerlink="" href="/"><img _ngcontent-eul-c95="" id="ped_logo_nav" src="assets/logos/PED_logo_white.svg" class="img-fluid"></a><button _ngcontent-eul-c95="" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation" class="navbar-toggler"><span _ngcontent-eul-c95="" class="navbar-toggler-icon"></span></button><div _ngcontent-eul-c95="" id="navbarSupportedContent" class="collapse navbar-collapse" aria-expanded="false" aria-hidden="true" style="display: none;"><ul _ngcontent-eul-c95="" class="navbar-nav mr-auto"><li _ngcontent-eul-c95="" class="nav-item"><a _ngcontent-eul-c95="" class="nav-link active btn"></a></li></ul><ul _ngcontent-eul-c95="" id="navbarButtons" class="navbar-nav navbar-right" style="min-height: 10px;"><li _ngcontent-eul-c95="" class="nav-item my-auto"><a _ngcontent-eul-c95="" routerlink="/browse" class="nav-link active btn" href="/browse">Browse</a></li><li _ngcontent-eul-c95="" class="nav-item my-auto"><a _ngcontent-eul-c95="" routerlink="/help" class="nav-link btn active" href="/help">Help</a></li><li _ngcontent-eul-c95="" class="nav-item my-auto"><a _ngcontent-eul-c95="" routerlink="/about" class="nav-link btn active" href="/about">About</a></li><li _ngcontent-eul-c95="" class="nav-item float-right my-auto"><a _ngcontent-eul-c95="" routerlink="/feedback" class="nav-link btn active" href="/feedback">Feedback</a></li><li _ngcontent-eul-c95="" class="nav-item float-right my-auto"><a _ngcontent-eul-c95="" routerlink="/deposition" class="nav-link btn active" href="/deposition">Deposition</a></li><li _ngcontent-eul-c95="" class="nav-item float-right my-auto"><!----></li></ul></div></nav></div></div></app-navbar></div><div _ngcontent-eul-c97="" class="container-fluid flex-grow" style="padding-top: 120px;"><router-outlet _ngcontent-eul-c97=""></router-outlet><app-entry-view-manager _nghost-eul-c137=""><!----><div _ngcontent-eul-c137=""><div _ngcontent-eul-c137="" class="container-fluid container-wide"><!----><!----></div><!----><!----><!----><!----><!----><app-public-entry-page _ngcontent-eul-c137="" _nghost-eul-c136=""><div _ngcontent-eul-c136="" class="container-fluid container-wide"><h3 _ngcontent-eul-c136="">PED00001 <span _ngcontent-eul-c136=""> - Structural ensemble of pSic1 (1-90) with phosphorylations at Thr5, Thr33, Thr45, Ser69, Ser76, Ser80 </span><!----></h3><div _ngcontent-eul-c136="" class="row mt-2"><div _ngcontent-eul-c136="" class="col"><div _ngcontent-eul-c136="" class="row"><div _ngcontent-eul-c136="" class="col-auto pr-2"><strong _ngcontent-eul-c136="">Data owner</strong></div><div _ngcontent-eul-c136=""><div _ngcontent-eul-c136="" class="col-auto pl-0 pr-2"><a _ngcontent-eul-c136="" target="_blank" style="white-space: nowrap;" href="https://orcid.org/">Tanja Mittag</a></div><!----></div><div _ngcontent-eul-c136=""><div _ngcontent-eul-c136="" class="col-auto pl-0 pr-2"><a _ngcontent-eul-c136="" target="_blank" style="white-space: nowrap;" href="https://orcid.org/">Joseph A. Marsh</a></div><!----></div><div _ngcontent-eul-c136=""><div _ngcontent-eul-c136="" class="col-auto pl-0 pr-2"><a _ngcontent-eul-c136="" target="_blank" style="white-space: nowrap;" href="https://orcid.org/">Alexander Grishaev</a></div><!----></div><div _ngcontent-eul-c136=""><div _ngcontent-eul-c136="" class="col-auto pl-0 pr-2"><a _ngcontent-eul-c136="" target="_blank" style="white-space: nowrap;" href="https://orcid.org/">Stephen Orlicky</a></div><!----></div><div _ngcontent-eul-c136=""><div _ngcontent-eul-c136="" class=
|
||
|
|
The Sic1 and pSic1 ensemble models comprised residues 1-90 of the full-length Sic1 amino acid sequence plus an N-terminal Gly-Ser sequence remaining after tag cleavage. Glutamate residues were used to represent the phosphorylated residues in pSic1 to facilitate use of TraDES (Feldman and Hogue, 2000). These glutamate residues were converted to the proper phosphorylated threonine or serine residues for electrostatic calculations. Three independent ensembles were calculated for each of free Sic1 and pSic1 and the pSic1 complex. Calculations were performed on a cluster of CPUs, with one main node performing the core conformational selection calculations and 8-12 nodes performing the iterative conformational sampling with CNS (Bru? nger et al., 1998), Unfoldtraj, and TraDES (Feldman and Hogue, 2000). The initial temperature for the ENSEMBLE calculations was set to 10,000 and decreased to 0.01 in 200,000 steps. The starting ensembles contained 200 structures and the number of conformers comprising the ensembles was decreased by one after each successful ENSEMBLE calculation in which full agreement with experimental restraints was achieved. Calculations were stopped when a smaller ensemble could not be successfully calculated within 72 hr. </p></div></div><!----><!----><!----><div _ngcontent-eul-c136="" class="row mt-1 mb-2"><div _ngcontent-eul-c136="" class="col"><strong _ngcontent-eul-c136="">Cross reference</strong><span _ngcontent-eul-c136=""><!----><a _ngcontent-eul-c136="" target="_blank" class="badge badge-external-link ml-1" href="https://disprot.org/DP00631"> disprot:DP00631 <i _ngcontent-eul-c136="" class="material-icons" style="font-size: small;">link</i></a><!----></span><!----></div></div><!----><div _ngcontent-eul-c136="" class="row"><div _ngcontent-eul-c136="" class="col"><div _ngcontent-eul-c136=""><app-feature-viewer-ensemble _ngcontent-eul-c136="" _nghost-eul-c133=""><div _ngcontent-eul-c133="" id="fv_obj_A" style="position: relative; padding: 0px; z-index: 2;"><foreignobject><div id="fvoverlay" data-container="body"></div></foreignobject><div class="fvtooltip" id="fvtooltip" style="opacity: 0; z-index: 1070;"></div><div class="fvcustomtooltip" id="fvcustomtooltip" style="opacity: 0; z-index: 1070;"></div><svg width="725" height="381px" id="svgContent" style="z-index: 2;"><g transform="translate(125,12)" id="tracks_container"><rect width="100%" height="100%" fill="gray"></rect><g class="x axis XAxis" transform="translate(0,351)" fill="none" font-size="10" font-family="sans-serif" text-anchor="middle"><path class="domain" stroke="currentColor" d="M2.5,6V0.5H581.5V6"></path><g class="tick" opacity="1" transform="translate(64.75806451612904,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">10</text></g><g class="tick" opacity="1" transform="translate(127.01612903225806,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">20</text></g><g class="tick" opacity="1" transform="translate(189.27419354838707,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">30</text></g><g class="tick" opacity="1" transform="translate(251.53225806451613,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">40</text></g><g class="tick" opacity="1" transform="translate(313.7903225806452,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">50</text></g><g class="tick" opacity="1" transform="translate(376.04838709677415,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">60</text></g><g class="tick" opacity="1" transform="translate(438.30645161290323,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">70</text></g><g class="tick" opacity="1" transform="translate(500.56451612903226,0)"><line stroke="currentColor" y2="6"></line><text fill="currentColor" y="9" dy="0.71em">80</text></g><g class="tick" opacity="1" transform="translate(562.8225806451613,0)"><line stroke="currentCo
|
||
|
|
<script src="runtime-es2015.66c79b9d36e7169e27b0.js" type="module"></script><script src="runtime-es5.66c79b9d36e7169e27b0.js" nomodule="" defer=""></script><script src="polyfills-es5.7f851a9e430b2b0cdf46.js" nomodule="" defer=""></script><script src="polyfills-es2015.4eb191482be2254421ff.js" type="module"></script><script src="scripts.d712956cb3638f64c0df.js" defer=""></script><script src="main-es2015.2b3675d6f63886eddce9.js" type="module"></script><script src="main-es5.2b3675d6f63886eddce9.js" nomodule="" defer=""></script>
|
||
|
|
|
||
|
|
<iframe scrolling="no" frameborder="0" allowtransparency="true" src="https://platform.twitter.com/widgets/widget_iframe.21f942bb866c2823339b839747a0c50c.html?origin=https%3A%2F%2Fproteinensemble.org" title="Twitter settings iframe" style="display: none;"></iframe><iframe id="rufous-sandbox" scrolling="no" frameborder="0" allowtransparency="true" allowfullscreen="true" style="position: absolute; visibility: hidden; display: none; width: 0px; height: 0px; padding: 0px; border: none;" title="Twitter analytics iframe"></iframe></body></html>
|